This chapter discusses the potential applications of fungi in the removal of organic pollutants from contaminated matrices. Reports on the transformation of organic pollutants by fungi abound in scientific literature; therefore, the present work is circumscribed to situations in which real polluted matrices were employed. Even though diverse fungi have been employed in bioremediation, the chapter focuses on the largely described ecological group of white-rot fungi. Among organic contaminants, two groups were mostly explored: the highly toxic pesticides, and the pharmaceutical therapeutic agents, the latter considered as emerging pollutants. The chapter outline includes three parts; the first one comprises an introduction describing the general characteristics of fungi, which make them interesting as potential agents for bioremediation. The second part presents some aspects of fungal-mediated liquid-phase (including enzymatic) and solid-phase approaches used in the treatment of pollutants. Finally, in the third part, a detailed description of the application of these processes is given, and the discussion emphasizes on the use of biopurification systems for the treatment of pesticides and the use of biopiles and slurry reactors to treat pharmaceuticals from matrices such as waste water or sewage sludge.